YRC Public Data Repository - Protein Structure Prediction

Protein:	gi\|220957602, gi...
Organism:	synthetic construct
Length:	210 amino acids
Reference:	Drew K, et al. (2011) The proteome folding project: Proteome-scale prediction of structure and function. Genome Res. 2011 Sep 16

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Top Sequence Alignment Hits

Listed below are up to the top 10 sequence alignment matches, by species, for the PSI-BLAST search against the protein sequence for gi|220957602, gi....

Description	E-value	Query Range	Subject Range
gi\|48124579 - gi\|48124579\|ref\|XP_396561.1\| PREDICTED: similar to Rpb5 CG11979-PA [Apis mellifera]	316.0	[0..1]	[210..1]
gi\|108872649, gi... - gi\|157128329\|ref\|XP_001661404.1\| DNA-directed RNA polymerase II [Aedes aegypti], gi\|108872649\|gb\|EAT... gi\|30174740, gi\|... - gi\|31235339\|ref\|XP_319221.1\| AGAP010064-PA [Anopheles gambiae str. PEST], gi\|30174740\|gb\|EAA43596.1\|... AGAP010064-PA - DNA-directed RNA polymerases I, II, and III subunit RPABC1\|protein_coding\|3R:48533978:48534680:1\|gen... gi\|167878475, gi... - gi\|170059825\|ref\|XP_001865530.1\| DNA-directed RNA polymerase II 23 kDa polypeptide [Culex quinquefas...	313.0	[0..1]	[210..1]
gi\|91087261 - gi\|91087261\|ref\|XP_975533.1\| PREDICTED: similar to AGAP010064-PA [Tribolium castaneum]	313.0	[0..1]	[210..1]
gi\|47216655 - gi\|47216655\|emb\|CAG04853.1\| unnamed protein product [Tetraodon nigroviridis]	310.0	[0..1]	[209..1]
gi\|38051843, gi\|... - gi\|38051843\|gb\|AAH60467.1\| MGC68604 protein [Xenopus laevis], gi\|148225220\|ref\|NP_001083516.1\| hypot... gi\|89272916, gi\|... - gi\|89272916\|emb\|CAJ82278.1\| polymerase (RNA) II (DNA directed) polypeptide E [Xenopus tropicalis], g...	310.0	[0..1]	[209..1]
gi\|2135016, gi\|1... - pir\|\|A32618 DNA-directed RNA polymerase (EC 2.7.7.6) II 23K chain [validated] - human, gi\|1060912\|d...	310.0	[0..1]	[209..1]
gi\|57525846, gi\|... - gi\|57525846\|ref\|NP_001003564.1\| polymerase (RNA) II (DNA directed) polypeptide E [Danio rerio], gi\|5...	310.0	[0..1]	[209..1]
gi\|54035366 - gb\|AAH83992.1\| Unknown (protein for MGC:98112) [Xenopus laevis] RPAB1_RAT - DNA-directed RNA polymerases I, II, and III subunit RPABC1 OS=Rattus norvegicus GN=Polr2e PE=2 SV=1 RPAB1_MOUSE - DNA-directed RNA polymerases I, II, and III subunit RPABC1 OS=Mus musculus GN=Polr2e PE=1 SV=1	310.0	[0..1]	[209..1]

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Predicted Domain #1

Region A:
Residues: [1-210]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MDDEAETYKL WRIRKTIMQL SHDRGYLVTQ DELDQTLEQF KEMFGDKPSE KRPARSDLIV  60
   61 LVAHNDDPTD QMFVFFPEEP KIGIKTIKTY CTRMQEENIH RAIVVVQGGM TPSAKQSLVD 120
  121 MAPKYILEQF LESELLINIT EHELVPEHVV MTVEEKQELL SRYKLKENML MRIQAGDPVA 180
  181 RYFGLKRGQV VKIIRSSETA GRYISYRLVC

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	75.0
Match:	1dzfA
Description:	Eukaryotic RPB5 N-terminal domain; Eukaryotic RPB5 C-terminal domain
Matching Structure (courtesy of the PDB):

TMHMM	2.0c	PSIPRED	v2.61
SignalP	3.0	COILS	1999
DISOPRED	v0.1	NCBI nr	06/2007
PSI-BLAST	2.2.18	FFAS	ffas03
PDB	06/2007	Pfam	22
HMMER	2.3.2

View Structure Prediction Details

Top Sequence Alignment Hits